For simple automated responses, Dennis' suggestion is sound. The vacation
program is also an ancient, honourable and extensively-tested piece of software to build simple autoresponses around, and it has all the necessary tests to avoid autoresponder storms (where two autoresponders start talking to each other, very very fast, and fill up your email spool).
For something more sophisticated, which you seem to be alluding to, where multiple emails are related to each other, something like RT might be a good place to start: emails to particular recipients are ducted into RT, and the first in the chain creates an autoresponse with a custom Subject: line, and as long as anyone who replies to that email preserves the RT token in the subject line, future replies will end up in the right thread inside the RT database.